Hi
ante-MMPBSA.py -h should list all the flags that are needed for generate
the necessary prmtops
Best Regards
ElMa
On Wed, 6 May 2020 at 18:58, Renato Araujo <renatoacufpa.gmail.com> wrote:
> Hi Elvis
>
> > Alternatively, you can prepare receptor.prmtop and ligand.prmtop using
> ante-MMPBSA.py from the complex.prmtop.
>
> What is the command I use to generate the files?
>
> Att.,
>
> Em qua., 6 de mai. de 2020 às 09:26, Elvis Martis <
> elvis_bcp.elvismartis.in>
> escreveu:
>
> > Hi
> > All the prmtop files are generated at the beginning.
> > Alternatively, you can prepare receptor.prmtop and ligand.prmtop using
> > ante-MMPBSA.py from the complex.prmtop.
> > The prmtop files do not contain coordinates, so they do not change after
> > you have completed all the phases of your simulation.
> >
> > Your input and commands look good.
> > I hope this helps.
> > Best Regards
> > ElMa
> >
> >
> >
> > On Wed, 6 May 2020 at 16:49, Renato Araujo <renatoacufpa.gmail.com>
> wrote:
> >
> > > Dear Amber users
> > >
> > > Please I need help
> > >
> > > I'm looking to perform the MMGBSA-DECOM calculation as my script
> mustard.
> > >
> > > MMGBSA-DECOM
> > > &general
> > > startframe=47500, endframe=50000, interval=1,
> > > verbose=2, keep_files=2, debug_printlevel=2,
> > > /
> > > &gb
> > > igb=5, saltcon=0.0,
> > > /
> > > &decomp
> > > idecomp=2, dec_verbose=1, csv_format=0, print_res="1-306"
> > > /
> > >
> > > According to the command
> > > mpirun -np 8 MMPBSA.py -O -i mmpbsa.in -o MMGBSA.dat -do
> > DECOMP_MMGBSA.dat
> > > -sp complex_solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> > > ligand.prmtop -y * .mdcrd
> > >
> > > I need the prmtop files:
> > > complex_solvated.prmtop
> > > complex.prmtop
> > > receiver.prmtop
> > > ligand.prmtop
> > >
> > > My doubt.
> > > These prmtop files are generated after the DM production phase or these
> > > prmtop files are generated there at the beginning (phases that we are
> > > preparing the system to minimize, heat and balance)
> > >
> > > Any help is welcome
> > >
> > > Renato Costa
> > > Federal Institute of Pará
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Wed May 06 2020 - 07:00:02 PDT
